Pokemon entered its third generation with the 2002 release of Pokemon Ruby and Sapphire for Game Boy Advance and continued with the Game Boy Advance remakes of Pokemon Red and Green, Pokemon FireRed and LeafGreen (Red and Green representing the original Japanese first generation games; territories outside Japan instead saw releases of Red and Blue). An enhanced version of Pokemon Ruby and Sapphire titled Pokemon Emerald followed after.

The third generation introduced 135 new Pokemon (starting with Treecko and ending with Deoxys) for a total of 386 species. It also features a more visually detailed environment compared to previous games, "natures" which affect Pokemon stats, a new 2-on-2 Pokemon battling mechanic, a special ability system applying to each Pokemon in battle, the Pokemon Contest sub-game, the new region of Hoenn, the ability to select the protagonist's gender and Secret Bases: customizable "rooms" where the player can display items they have collected in-game and battle against real friends. Secret Bases can be found in bushes, trees, or small cave openings in landscapes by using the Pokemon move, Secret Power, which can be taught to virtually all Pokemon. However, this generation also garnered some criticism for leaving out several gameplay features, including the day-and-night system introduced in the previous generation (which was removed due to internal-battery save problems), and it was also the first installment that encouraged the player to collect merely a selected assortment of the total number of Pokemon rather than every existing species (202 out of 386 species are catchable in the Ruby and Sapphire versions). Around this time that the franchise was regaining its popularity and it managed to ship over 100 million games worldwide.

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